The following will go through converting the Crystals restraints list into
Fullprof format, inputting this into GSAS format; then performing the restrained
refinement.
(Refer to the CCP14 Based Fullprof Tutorial Pages for download information on Fullprof) At present (October 2000), converting the Crystals restraints list is done manually and only bond-restraints are supported by Fullprof (no bond-angle restraints/planar restraints). Again, it is important that the restraint commands you generated in Crystals matches the atom labels in Fullprof or mayhem and chaos will result. Also refer to Randomly Perturbing Atomic Positions in Crystals. This can be relevant for successfully performing DLS and refinement involving pseudo-symmetry. |
Crystals Restraints List from previous tutorial pageDIST 1.352,.01= O(2) TO C(12) DIST 1.432,.01= O(3) TO C(17) DIST 1.259,.01= O(4) TO C(22) DIST 1.234,.01= O(5) TO C(24) DIST 1.422,.01= O(6) TO C(25) DIST 1.330,.01= O(7) TO C(26) DIST 1.276,.01= O(8) TO C(28) DIST 1.313,.01= O(9) TO C(30) DIST 1.494,.01= N(10) TO C(21) DIST 1.490,.01= N(10) TO C(32) DIST 1.491,.01= N(10) TO C(33) DIST 1.301,.01= N(11) TO C(30) DIST 1.386,.01= C(12) TO C(13) DIST 1.405,.01= C(12) TO C(29) DIST 1.357,.01= C(13) TO C(14) DIST 1.399,.01= C(14) TO C(15) DIST 1.375,.01= C(15) TO C(16) DIST 1.534,.01= C(16) TO C(17) DIST 1.422,.01= C(16) TO C(29) DIST 1.540,.01= C(17) TO C(18) DIST 1.516,.01= C(17) TO C(31) DIST 1.526,.01= C(18) TO C(19) DIST 1.512,.01= C(18) TO C(27) DIST 1.534,.01= C(19) TO C(20) DIST 1.538,.01= C(20) TO C(21) DIST 1.522,.01= C(20) TO C(25) DIST 1.522,.01= C(21) TO C(22) DIST 1.403,.01= C(22) TO C(23) DIST 1.427,.01= C(23) TO C(24) DIST 1.435,.01= C(23) TO C(30) DIST 1.552,.01= C(24) TO C(25) DIST 1.508,.01= C(25) TO C(26) DIST 1.354,.01= C(26) TO C(27) DIST 1.445,.01= C(27) TO C(28) DIST 1.451,.01= C(28) TO C(29) |
Restraints in Fullprof FormatThe Fullprof dis parameter (to the right of the number of atoms in the phase) is set to the number of restraints, in this case "35". O2 C12 1 0.00000 0.00000 0.00000 1.35200 0.01000 O3 C17 1 0.00000 0.00000 0.00000 1.43200 0.01000 O4 C22 1 0.00000 0.00000 0.00000 1.25900 0.01000 O5 C24 1 0.00000 0.00000 0.00000 1.23400 0.01000 O6 C25 1 0.00000 0.00000 0.00000 1.42200 0.01000 O7 C26 1 0.00000 0.00000 0.00000 1.33000 0.01000 O8 C28 1 0.00000 0.00000 0.00000 1.27600 0.01000 O9 C30 1 0.00000 0.00000 0.00000 1.31300 0.01000 N10 C21 1 0.00000 0.00000 0.00000 1.49400 0.01000 N10 C32 1 0.00000 0.00000 0.00000 1.49000 0.01000 N10 C33 1 0.00000 0.00000 0.00000 1.49100 0.01000 N11 C30 1 0.00000 0.00000 0.00000 1.30100 0.01000 C12 C13 1 0.00000 0.00000 0.00000 1.38600 0.01000 C12 C29 1 0.00000 0.00000 0.00000 1.40500 0.01000 C13 C14 1 0.00000 0.00000 0.00000 1.35700 0.01000 C14 C15 1 0.00000 0.00000 0.00000 1.39900 0.01000 C15 C16 1 0.00000 0.00000 0.00000 1.37500 0.01000 C16 C17 1 0.00000 0.00000 0.00000 1.53400 0.01000 C16 C29 1 0.00000 0.00000 0.00000 1.42200 0.01000 C17 C18 1 0.00000 0.00000 0.00000 1.54000 0.01000 C17 C31 1 0.00000 0.00000 0.00000 1.51600 0.01000 C18 C19 1 0.00000 0.00000 0.00000 1.52600 0.01000 C18 C27 1 0.00000 0.00000 0.00000 1.51200 0.01000 C19 C20 1 0.00000 0.00000 0.00000 1.53400 0.01000 C20 C21 1 0.00000 0.00000 0.00000 1.53800 0.01000 C20 C25 1 0.00000 0.00000 0.00000 1.52200 0.01000 C21 C22 1 0.00000 0.00000 0.00000 1.52200 0.01000 C22 C23 1 0.00000 0.00000 0.00000 1.40300 0.01000 C23 C24 1 0.00000 0.00000 0.00000 1.42700 0.01000 C23 C30 1 0.00000 0.00000 0.00000 1.43500 0.01000 C24 C25 1 0.00000 0.00000 0.00000 1.55200 0.01000 C25 C26 1 0.00000 0.00000 0.00000 1.50800 0.01000 C26 C27 1 0.00000 0.00000 0.00000 1.35400 0.01000 C27 C28 1 0.00000 0.00000 0.00000 1.44500 0.01000 C28 C29 1 0.00000 0.00000 0.00000 1.45100 0.01000
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Fullprof Input File(For comparison with single crystal results of tetracycline refer: "Tetracycline hydrochloride: a synchrotron micro-crystal study" Clegg W. & Teat S.J. Acta Cryst., C56 , 1343-1345 (2000)) Paste the restraints into the Fullprof file.
COMM Tetracycline C22H24N2O8HCl P212121 ! Files => DAT-file: refine, PCR-file: refine !Job Npr Nph Nba Nex Nsc Nor Dum Iwg Ilo Ias Res Ste Nre Cry Uni Cor Opt Aut 0 5 1 26 0 0 1 1 0 0 1 0 0 0 0 0 0 0 0 ! !Ipr Ppl Ioc Mat Pcr Ls1 Ls2 Ls3 Syo Prf Ins Rpa Sym Hkl Fou Sho Ana 0 0 1 0 1 0 0 0 1 1 0 1 0 1 2 0 0 ! ! lambda1 Lambda2 Ratio Bkpos Wdt Cthm muR AsyLim Rpolarz ->Patt# 1 1.540560 1.544390 0.5000 90.0000 12.0000 0.7998 0.0000 34.50 0.5000 ! !NCY Eps R_at R_an R_pr R_gl Thmin Step Thmax PSD Sent0 9 0.01 0.50 0.50 0.50 0.50 7.0000 0.0200 100.0000 0.000 0.000 ! !2Theta/TOF/E(Kev) Background for Pattern# 1 6.850 3035.166 7.917 2648.353 12.312 1826.374 14.258 1729.671 17.209 1584.617 18.967 1584.617 25.496 1536.266 29.639 1778.023 34.347 1923.077 38.428 1778.023 45.208 1923.077 47.092 1729.671 50.725 1550.550 56.585 1110.989 58.343 1005.495 61.356 970.330 64.453 952.748 69.057 882.418 73.158 864.836 78.097 847.253 80.859 847.253 84.877 864.836 87.640 759.341 91.490 636.264 94.922 636.264 100.279 565.935 ! ! 104 !Number of refined parameters ! ! Zero Code Sycos Code Sysin Code Lambda Code MORE ->Patt# 1 -0.08755 0.00 0.00000 0.00 0.00000 0.00 0.000000 0.00 0 !------------------------------------------------------------------------------- ! Data for PHASE number: 1 ==> Current R_Bragg for Pattern# 1: 19.39 !------------------------------------------------------------------------------- C22H24N2O8HCl ! !Nat Dis Mom Pr1 Pr2 Pr3 Jbt Irf Isy Str Furth ATZ Nvk Npr More 33 35 0 1.0 0.0 0.0 0 0 0 0 0 0.00 0 5 0 ! P 21 21 21 <--Space group symbol !Atom Typ X Y Z Biso Occ In Fin N_t Poi /Codes Cl1 CL 0.92697 0.42257 -0.00119 2.34344 1.00000 0 0 0 0 21.00 31.00 41.00 51.00 0.00 O2 O 0.01188 0.37313 0.43554 2.90609 1.00000 0 0 0 0 61.00 71.00 81.00 1031.00 0.00 O3 O 0.14336 0.45564 0.12582 2.90609 1.00000 0 0 0 0 91.00 101.00 111.00 1031.00 0.00 O4 O 0.75524 0.64890 0.07187 2.90609 1.00000 0 0 0 0 121.00 131.00 141.00 1031.00 0.00 O5 O 0.36201 0.71889 0.18555 2.90609 1.00000 0 0 0 0 151.00 161.00 171.00 1031.00 0.00 O6 O 0.57821 0.60724 0.30151 2.90609 1.00000 0 0 0 0 181.00 191.00 201.00 1031.00 0.00 O7 O 0.35005 0.61270 0.35933 2.90609 1.00000 0 0 0 0 211.00 221.00 231.00 1031.00 0.00 O8 O 0.16567 0.50358 0.38857 2.90609 1.00000 0 0 0 0 241.00 251.00 261.00 1031.00 0.00 O9 O 0.66186 0.81635 0.04394 2.90609 1.00000 0 0 0 0 271.00 281.00 291.00 1031.00 0.00 N10 N 0.75288 0.45777 0.13838 1.58174 1.00000 0 0 0 0 301.00 311.00 321.00 1041.00 0.00 N11 N 0.46049 0.85949 0.08242 1.58174 1.00000 0 0 0 0 331.00 341.00 351.00 1041.00 0.00 C12 C 0.01987 0.32864 0.36337 2.86195 1.00000 0 0 0 0 361.00 371.00 381.00 651.00 0.00 C13 C -0.04760 0.24520 0.34562 2.86195 1.00000 0 0 0 0 391.00 401.00 411.00 651.00 0.00 C14 C -0.03888 0.19790 0.26857 2.86195 1.00000 0 0 0 0 421.00 431.00 441.00 651.00 0.00 C15 C 0.03547 0.23002 0.20638 2.86195 1.00000 0 0 0 0 451.00 461.00 471.00 651.00 0.00 C16 C 0.10846 0.31727 0.22146 2.86195 1.00000 0 0 0 0 481.00 491.00 501.00 651.00 0.00 C17 C 0.19532 0.36556 0.15400 2.86195 1.00000 0 0 0 0 511.00 521.00 531.00 651.00 0.00 C18 C 0.31453 0.39376 0.20113 2.86195 1.00000 0 0 0 0 541.00 551.00 561.00 651.00 0.00 C19 C 0.41903 0.43295 0.14460 2.86195 1.00000 0 0 0 0 571.00 581.00 591.00 651.00 0.00 C20 C 0.52797 0.48451 0.19053 2.86195 1.00000 0 0 0 0 601.00 611.00 621.00 651.00 0.00 C21 C 0.63398 0.51058 0.12199 2.86195 1.00000 0 0 0 0 631.00 641.00 661.00 651.00 0.00 C22 C 0.65855 0.62653 0.10963 2.86195 1.00000 0 0 0 0 671.00 681.00 691.00 651.00 0.00 C23 C 0.56261 0.69709 0.12812 2.86195 1.00000 0 0 0 0 701.00 711.00 721.00 651.00 0.00 C24 C 0.46096 0.67040 0.18331 2.86195 1.00000 0 0 0 0 731.00 741.00 751.00 651.00 0.00 C25 C 0.48293 0.57570 0.24342 2.86195 1.00000 0 0 0 0 761.00 771.00 781.00 651.00 0.00 C26 C 0.37020 0.55014 0.28988 2.86195 1.00000 0 0 0 0 791.00 801.00 811.00 651.00 0.00 C27 C 0.28989 0.46988 0.27043 2.86195 1.00000 0 0 0 0 821.00 831.00 841.00 651.00 0.00 C28 C 0.19187 0.44584 0.32695 2.86195 1.00000 0 0 0 0 851.00 861.00 871.00 651.00 0.00 C29 C 0.10202 0.36889 0.30115 2.86195 1.00000 0 0 0 0 881.00 891.00 901.00 651.00 0.00 C30 C 0.55524 0.78952 0.07658 2.86195 1.00000 0 0 0 0 911.00 921.00 931.00 651.00 0.00 C31 C 0.21594 0.29539 0.07977 2.86195 1.00000 0 0 0 0 941.00 951.00 961.00 651.00 0.00 C32 C 0.73501 0.34343 0.13524 2.86195 1.00000 0 0 0 0 971.00 981.00 991.00 651.00 0.00 C33 C 0.80700 0.48587 0.22202 2.86195 1.00000 0 0 0 0 1001.00 1011.00 1021.00 651.00 0.00 !-------> Profile Parameters for Pattern # 1 ! Scale Shape1 Bov Str1 Str2 Str3 Strain-Model 0.21068E-02 0.4572 0.0000 0.0000 0.0000 0.0000 0 11.00000 0.00 0.00 0.00 0.00 0.00 ! U V W X Y GauSiz LorSiz Size-Model 0.31737 -0.12372 0.03987 0.00000 0.00000 0.00000 0.00000 0 101.00 0.00 31.00 0.00 0.00 0.00 0.00 ! a b c alpha beta gamma 10.969498 12.847066 15.712444 90.000000 90.000000 90.000000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 ! Pref1 Pref2 Asy1 Asy2 Asy3 Asy4 1.00000 0.00000 0.09272 0.06000 0.00000 0.00000 0.00 0.00 0.00 0.00 0.00 0.00 ! Soft distance constraints: O2 C12 1 0.00000 0.00000 0.00000 1.35200 0.01000 O3 C17 1 0.00000 0.00000 0.00000 1.43200 0.01000 O4 C22 1 0.00000 0.00000 0.00000 1.25900 0.01000 O5 C24 1 0.00000 0.00000 0.00000 1.23400 0.01000 O6 C25 1 0.00000 0.00000 0.00000 1.42200 0.01000 O7 C26 1 0.00000 0.00000 0.00000 1.33000 0.01000 O8 C28 1 0.00000 0.00000 0.00000 1.27600 0.01000 O9 C30 1 0.00000 0.00000 0.00000 1.31300 0.01000 N10 C21 1 0.00000 0.00000 0.00000 1.49400 0.01000 N10 C32 1 0.00000 0.00000 0.00000 1.49000 0.01000 N10 C33 1 0.00000 0.00000 0.00000 1.49100 0.01000 N11 C30 1 0.00000 0.00000 0.00000 1.30100 0.01000 C12 C13 1 0.00000 0.00000 0.00000 1.38600 0.01000 C12 C29 1 0.00000 0.00000 0.00000 1.40500 0.01000 C13 C14 1 0.00000 0.00000 0.00000 1.35700 0.01000 C14 C15 1 0.00000 0.00000 0.00000 1.39900 0.01000 C15 C16 1 0.00000 0.00000 0.00000 1.37500 0.01000 C16 C17 1 0.00000 0.00000 0.00000 1.53400 0.01000 C16 C29 1 0.00000 0.00000 0.00000 1.42200 0.01000 C17 C18 1 0.00000 0.00000 0.00000 1.54000 0.01000 C17 C31 1 0.00000 0.00000 0.00000 1.51600 0.01000 C18 C19 1 0.00000 0.00000 0.00000 1.52600 0.01000 C18 C27 1 0.00000 0.00000 0.00000 1.51200 0.01000 C19 C20 1 0.00000 0.00000 0.00000 1.53400 0.01000 C20 C21 1 0.00000 0.00000 0.00000 1.53800 0.01000 C20 C25 1 0.00000 0.00000 0.00000 1.52200 0.01000 C21 C22 1 0.00000 0.00000 0.00000 1.52200 0.01000 C22 C23 1 0.00000 0.00000 0.00000 1.40300 0.01000 C23 C24 1 0.00000 0.00000 0.00000 1.42700 0.01000 C23 C30 1 0.00000 0.00000 0.00000 1.43500 0.01000 C24 C25 1 0.00000 0.00000 0.00000 1.55200 0.01000 C25 C26 1 0.00000 0.00000 0.00000 1.50800 0.01000 C26 C27 1 0.00000 0.00000 0.00000 1.35400 0.01000 C27 C28 1 0.00000 0.00000 0.00000 1.44500 0.01000 C28 C29 1 0.00000 0.00000 0.00000 1.45100 0.01000 |
Restrained Refinement in FullprofThe Fullprof *.out output file will tell you what is going on with respect to the bond length restraints and if you have made any obvious mistakes setting things up.=> Distance constraints: Dobs Dcalc diff/sigma (O2 - C12 ): 1.35200 1.33918 1.28200 (O3 - C17 ): 1.43200 1.44425 -1.22492 (O4 - C22 ): 1.25900 1.25923 -0.02342 (O5 - C24 ): 1.23400 1.27322 -3.92196 (O6 - C25 ): 1.42200 1.44513 -2.31262 (O7 - C26 ): 1.33000 1.37402 -4.40164 (O8 - C28 ): 1.27600 1.29485 -1.88483 (O9 - C30 ): 1.31300 1.32626 -1.32631 (N10 - C21 ): 1.49400 1.49864 -0.46387 (N10 - C32 ): 1.49000 1.48344 0.65643 (N10 - C33 ): 1.49100 1.46163 2.93682 (N11 - C30 ): 1.30100 1.34755 -4.65486 (C12 - C13 ): 1.38600 1.37961 0.63871 (C12 - C29 ): 1.40500 1.43496 -2.99565 (C13 - C14 ): 1.35700 1.35754 -0.05361 (C14 - C15 ): 1.39900 1.41365 -1.46538 (C15 - C16 ): 1.37500 1.39229 -1.72884 (C16 - C17 ): 1.53400 1.54902 -1.50199 (C16 - C29 ): 1.42200 1.45817 -3.61701 (C17 - C18 ): 1.54000 1.52876 1.12411 (C17 - C31 ): 1.51600 1.49568 2.03242 (C18 - C19 ): 1.52600 1.53847 -1.24725 (C18 - C27 ): 1.51200 1.54576 -3.37646 (C19 - C20 ): 1.53400 1.52490 0.90995 (C20 - C21 ): 1.53800 1.54776 -0.97597 (C20 - C25 ): 1.52200 1.56787 -4.58719 (C21 - C22 ): 1.52200 1.55911 -3.71107 (C22 - C23 ): 1.40300 1.44134 -3.83443 (C23 - C24 ): 1.42700 1.48698 -5.99785 (C23 - C30 ): 1.43500 1.47896 -4.39645 (C24 - C25 ): 1.55200 1.58359 -3.15930 (C25 - C26 ): 1.50800 1.53789 -2.98923 (C26 - C27 ): 1.35400 1.41101 -5.70073 (C27 - C28 ): 1.44500 1.46845 -2.34495 (C28 - C29 ): 1.45100 1.47536 -2.43574 |
GSAS GUI WINORTEP by Louis Farrugia to examine the Structure and resulting bond lengths and angles during the refinementUsing Ortep-3 you can quickly load the Fullprof *.pcr file and check that the bond length and angle restraints are doing what you think they should be doing (using the Calculate menu option). You can also keep a graphical eye on the thermals.
In the following case, thermals are quite large, possibly due to poorly defined manual background. Switching to a refined background might be a better thing to do here.
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Looking at the Rietveld plot in Winplotr
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Further OptionsYou may want to re-import the structure back into Crystals (using Ortep-3) to allow very easy placement of hydrogens (Structure, Add Hydrogens); as well as possible validation with the CSD database to check that bond-length and angles are consistent with structures already in the Cambridge Database. A "might happen" feature for a future version of Crystals is to generate idealised bond lengths and bond angles based on the cambridge database in a similar way to how Crystals presently does the CSD validation. |